VariantFiltering
Filtering of coding and non-coding genetic variants
Bioconductor version: 3.23 · Package version: 1.48.0
Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("VariantFiltering")Details
| Maintainer | Robert Castelo <robert.castelo@upf.edu> |
| Author | Robert Castelo [aut, cre], Dei Martinez Elurbe [ctb], Pau Puigdevall [ctb], Joan Fernandez [ctb] |
| License | Artistic-2.0 |
| URL | https://github.com/rcastelo/VariantFiltering |
| Bug Reports | https://github.com/rcastelo/VariantFiltering/issues |
| Downloads rank | 757 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | VariantFiltering_1.48.0.tar.gz |
| Windows binary (x86_64) | VariantFiltering_1.48.0.zip |
| macOS binary (arm64) | VariantFiltering_1.48.0.tgz |
| macOS binary (x86_64) | VariantFiltering_1.48.0.tgz |
Dependencies
Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29)
Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.7), Biostrings (>= 2.77.2), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), GenomicFeatures (>= 1.61.4), Rsamtools (>= 2.25.1), BSgenome (>= 1.77.1), GenomicScores (>= 2.21.4), Gviz (>= 1.53.1), shiny, shinythemes, shinyjs, DT, shinyTree
LinkingTo: S4Vectors, IRanges, XVector, Biostrings
Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137